Does reinstalling OS reset Libraries or System/Library?

Does reinstalling OS reset Libraries or System/Library?
I'm having some problems with the Java Liraries not being set up correctly or something. I've reinstalled SL to try and solve this problem, but I'm not sure if it's doing anything.
So does it reset the user's library or reset the system/library?
Cheers

If you reinstall using an install disc and choose upgrade, it REPLACES all OS components, wiping out the current ones, and replaces generic Apple apps, such as TextEdit, Safari, Terminal, etc. It doesn't touch anything in the user's directory or network settings. To bring the apps and OS up to its latest version, install the latest COMBO update. Finally, run Software Update to get any missing items.

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    It's just a status message, albeit a misleading one, and can be ignored.
    http://support.apple.com/kb/TS1448
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    What does this mean?  What should I do?
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    You don't even have to type more than 8 letters:

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    I get this message often when updating things. I have told Small Dog Computer where I buy my stuff, and they didn't have an answer. Thanks in advance.
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    I clicked on ok. The box behind said updates were installed and I didn't have any problems.  Is this something that needs attention?  Thank you.

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    What does this message mean? "Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired"  I get this when I try to repair permissions in disk utility.

    It's an innocuous error you can ignore. It was introduced with previous updates for ARD and/or Java before Lion. These are messages, not errors. They will cause no harm, and they will be repeated each time you repair permissions.

  • I reinstalled my computer's operating system.  How do I transfer music from my Ipod to my music library?  It transfered some, but not all my music.  I authorized the computer, but it did not help.

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